3MGQ
Binding of Nickel ions to the Nucleosome Core Particle
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0000786 | cellular_component | nucleosome |
A | 0003677 | molecular_function | DNA binding |
A | 0005515 | molecular_function | protein binding |
A | 0005634 | cellular_component | nucleus |
A | 0005654 | cellular_component | nucleoplasm |
A | 0005694 | cellular_component | chromosome |
A | 0030527 | molecular_function | structural constituent of chromatin |
A | 0046982 | molecular_function | protein heterodimerization activity |
B | 0000786 | cellular_component | nucleosome |
B | 0003677 | molecular_function | DNA binding |
B | 0005515 | molecular_function | protein binding |
B | 0005634 | cellular_component | nucleus |
B | 0005694 | cellular_component | chromosome |
B | 0006334 | biological_process | nucleosome assembly |
B | 0030527 | molecular_function | structural constituent of chromatin |
B | 0046982 | molecular_function | protein heterodimerization activity |
C | 0000786 | cellular_component | nucleosome |
C | 0003677 | molecular_function | DNA binding |
C | 0005634 | cellular_component | nucleus |
C | 0005694 | cellular_component | chromosome |
C | 0030527 | molecular_function | structural constituent of chromatin |
C | 0046982 | molecular_function | protein heterodimerization activity |
D | 0000786 | cellular_component | nucleosome |
D | 0003677 | molecular_function | DNA binding |
D | 0005515 | molecular_function | protein binding |
D | 0005634 | cellular_component | nucleus |
D | 0005694 | cellular_component | chromosome |
D | 0030527 | molecular_function | structural constituent of chromatin |
D | 0046982 | molecular_function | protein heterodimerization activity |
E | 0000786 | cellular_component | nucleosome |
E | 0003677 | molecular_function | DNA binding |
E | 0005515 | molecular_function | protein binding |
E | 0005634 | cellular_component | nucleus |
E | 0005654 | cellular_component | nucleoplasm |
E | 0005694 | cellular_component | chromosome |
E | 0030527 | molecular_function | structural constituent of chromatin |
E | 0046982 | molecular_function | protein heterodimerization activity |
F | 0000786 | cellular_component | nucleosome |
F | 0003677 | molecular_function | DNA binding |
F | 0005515 | molecular_function | protein binding |
F | 0005634 | cellular_component | nucleus |
F | 0005694 | cellular_component | chromosome |
F | 0006334 | biological_process | nucleosome assembly |
F | 0030527 | molecular_function | structural constituent of chromatin |
F | 0046982 | molecular_function | protein heterodimerization activity |
G | 0000786 | cellular_component | nucleosome |
G | 0003677 | molecular_function | DNA binding |
G | 0005634 | cellular_component | nucleus |
G | 0005694 | cellular_component | chromosome |
G | 0030527 | molecular_function | structural constituent of chromatin |
G | 0046982 | molecular_function | protein heterodimerization activity |
H | 0000786 | cellular_component | nucleosome |
H | 0003677 | molecular_function | DNA binding |
H | 0005515 | molecular_function | protein binding |
H | 0005634 | cellular_component | nucleus |
H | 0005694 | cellular_component | chromosome |
H | 0030527 | molecular_function | structural constituent of chromatin |
H | 0046982 | molecular_function | protein heterodimerization activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI E 136 |
Chain | Residue |
D | VAL45 |
E | ASP77 |
site_id | AC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE NI J 74 |
Chain | Residue |
I | DG-28 |
I | DT67 |
J | DG27 |
site_id | AC3 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI I 74 |
Chain | Residue |
I | DG61 |
site_id | AC4 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI I 75 |
Chain | Residue |
I | DG-3 |
site_id | AC5 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 75 |
Chain | Residue |
J | DG48 |
site_id | AC6 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 76 |
Chain | Residue |
J | DG-3 |
site_id | AC7 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 77 |
Chain | Residue |
J | DG61 |
site_id | AC8 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE NI D 123 |
Chain | Residue |
D | GLU102 |
D | HIS106 |
F | HIS18 |
site_id | AC9 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI I 76 |
Chain | Residue |
I | DG48 |
site_id | BC1 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI H 123 |
Chain | Residue |
H | HIS79 |
site_id | BC2 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI I 77 |
Chain | Residue |
I | DA26 |
I | DG27 |
site_id | BC3 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 78 |
Chain | Residue |
J | DG8 |
site_id | BC4 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI I 78 |
Chain | Residue |
I | DG-56 |
site_id | BC5 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 79 |
Chain | Residue |
J | DG-6 |
site_id | BC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE NI H 124 |
Chain | Residue |
H | GLU102 |
H | LYS105 |
H | HIS106 |
site_id | BC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI J 80 |
Chain | Residue |
J | DA29 |
J | DG30 |
site_id | BC8 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 81 |
Chain | Residue |
J | DG-56 |
site_id | BC9 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI D 124 |
Chain | Residue |
D | HIS79 |
site_id | CC1 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE NI I 80 |
Chain | Residue |
I | DG-35 |
I | DG-34 |
I | NI86 |
site_id | CC2 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 82 |
Chain | Residue |
J | DG5 |
site_id | CC3 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI I 81 |
Chain | Residue |
I | DA29 |
site_id | CC4 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 83 |
Chain | Residue |
J | DG71 |
site_id | CC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE NI I 82 |
Chain | Residue |
I | DG24 |
I | DG25 |
I | NI89 |
site_id | CC6 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI J 84 |
Chain | Residue |
J | DG-35 |
J | DG-34 |
site_id | CC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI J 85 |
Chain | Residue |
J | DG24 |
J | DG25 |
site_id | CC8 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI I 83 |
Chain | Residue |
I | DG71 |
site_id | CC9 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI I 84 |
Chain | Residue |
I | DG64 |
I | DG65 |
site_id | DC1 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 86 |
Chain | Residue |
J | DA-70 |
site_id | DC2 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI H 125 |
Chain | Residue |
H | HIS46 |
site_id | DC3 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 87 |
Chain | Residue |
J | DG-34 |
site_id | DC4 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI J 88 |
Chain | Residue |
I | DG-15 |
J | DG14 |
site_id | DC5 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI I 85 |
Chain | Residue |
I | DG-6 |
site_id | DC6 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI I 86 |
Chain | Residue |
I | DG-34 |
I | NI80 |
site_id | DC7 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE NI I 87 |
Chain | Residue |
I | DG58 |
I | DC59 |
I | NI91 |
J | DG-59 |
site_id | DC8 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI F 103 |
Chain | Residue |
F | ASP24 |
site_id | DC9 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI A 136 |
Chain | Residue |
A | ASP77 |
site_id | EC1 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 89 |
Chain | Residue |
J | DA-19 |
site_id | EC2 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI J 90 |
Chain | Residue |
J | DG52 |
site_id | EC3 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI C 120 |
Chain | Residue |
C | ASP90 |
site_id | EC4 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI I 88 |
Chain | Residue |
I | DG52 |
site_id | EC5 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI J 91 |
Chain | Residue |
I | DC-30 |
J | DA-70 |
site_id | EC6 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE NI G 120 |
Chain | Residue |
G | ASP90 |
site_id | EC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE NI I 89 |
Chain | Residue |
I | DG24 |
I | DG25 |
I | NI82 |
site_id | EC8 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI I 91 |
Chain | Residue |
I | DT57 |
I | NI87 |
site_id | EC9 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE NI J 105 |
Chain | Residue |
J | DG64 |
J | DG65 |
site_id | FC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CL G 3145 |
Chain | Residue |
G | GLY44 |
G | GLY46 |
G | ALA47 |
H | THR87 |
H | SER88 |
site_id | FC2 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL C 3146 |
Chain | Residue |
C | GLY46 |
C | ALA47 |
D | THR87 |
D | SER88 |
site_id | FC3 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL A 3147 |
Chain | Residue |
A | PRO121 |
A | LYS122 |
site_id | FC4 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL E 3148 |
Chain | Residue |
E | PRO121 |
E | LYS122 |
Functional Information from PROSITE/UniProt
site_id | PS00046 |
Number of Residues | 7 |
Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
Chain | Residue | Details |
C | ALA21-VAL27 |
site_id | PS00047 |
Number of Residues | 5 |
Details | HISTONE_H4 Histone H4 signature. GAKRH |
Chain | Residue | Details |
B | GLY14-HIS18 |
site_id | PS00322 |
Number of Residues | 7 |
Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
Chain | Residue | Details |
A | LYS14-LEU20 |
site_id | PS00357 |
Number of Residues | 23 |
Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
Chain | Residue | Details |
D | ARG89-GLY111 |
site_id | PS00959 |
Number of Residues | 9 |
Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
Chain | Residue | Details |
A | PRO66-ILE74 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 8 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P0C1H4 |
Chain | Residue | Details |
D | LYS2 | |
D | LYS9 | |
D | LYS12 | |
D | LYS17 | |
H | LYS2 | |
H | LYS9 | |
H | LYS12 | |
H | LYS17 |
site_id | SWS_FT_FI2 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:12757711 |
Chain | Residue | Details |
D | SER11 | |
H | SER11 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807 |
Chain | Residue | Details |
D | SER109 | |
H | SER109 |
site_id | SWS_FT_FI4 |
Number of Residues | 4 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P0C1H4 |
Chain | Residue | Details |
D | LYS117 | |
F | LYS5 | |
H | LYS117 |
site_id | SWS_FT_FI5 |
Number of Residues | 8 |
Details | MOD_RES: N6-propionyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | LYS8 | |
B | LYS16 | |
B | LYS44 | |
B | LYS79 | |
F | LYS8 | |
F | LYS16 | |
F | LYS44 | |
F | LYS79 |
site_id | SWS_FT_FI6 |
Number of Residues | 4 |
Details | MOD_RES: N6-methyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | LYS12 | |
B | LYS20 | |
F | LYS12 | |
F | LYS20 |
site_id | SWS_FT_FI7 |
Number of Residues | 4 |
Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | LYS31 | |
B | LYS91 | |
F | LYS31 | |
F | LYS91 |
site_id | SWS_FT_FI8 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine; by PAK2 => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | SER47 | |
F | SER47 |
site_id | SWS_FT_FI9 |
Number of Residues | 4 |
Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | TYR51 | |
B | TYR88 | |
F | TYR51 | |
F | TYR88 |
site_id | SWS_FT_FI10 |
Number of Residues | 2 |
Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | LYS59 | |
E | LYS64 | |
F | LYS59 | |
A | LYS27 | |
A | LYS36 | |
A | LYS64 | |
E | LYS18 | |
E | LYS23 | |
E | LYS27 | |
E | LYS36 |
site_id | SWS_FT_FI11 |
Number of Residues | 2 |
Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | LYS77 | |
F | LYS77 |
site_id | SWS_FT_FI12 |
Number of Residues | 2 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
B | LYS31 | |
F | LYS31 |
site_id | SWS_FT_FI13 |
Number of Residues | 4 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P62805 |
Chain | Residue | Details |
A | LYS37 | |
B | LYS91 | |
F | LYS91 |
site_id | SWS_FT_FI14 |
Number of Residues | 2 |
Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | TYR41 | |
E | TYR41 |
site_id | SWS_FT_FI15 |
Number of Residues | 4 |
Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 |
Chain | Residue | Details |
A | LYS56 | |
A | LYS79 | |
E | LYS56 | |
E | LYS79 |
site_id | SWS_FT_FI16 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | SER57 | |
E | SER57 |
site_id | SWS_FT_FI17 |
Number of Residues | 4 |
Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | THR80 | |
A | THR107 | |
E | THR80 | |
E | THR107 |
site_id | SWS_FT_FI18 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
Chain | Residue | Details |
A | SER86 | |
E | SER86 |
site_id | SWS_FT_FI19 |
Number of Residues | 2 |
Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | LYS115 | |
E | LYS115 |
site_id | SWS_FT_FI20 |
Number of Residues | 2 |
Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | LYS122 | |
E | LYS122 |
site_id | SWS_FT_FI21 |
Number of Residues | 2 |
Details | LIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | CYS110 | |
E | CYS110 |